macs2 for centromere chip-seq peak calling

Question

[Alex S]

I am trying to locate the centromere in one of our genome assemblies using chip-seq data from CenH3.

I am performing the peak calling using macs2 peakcall function using bam files from bowtie2 (treatment and control). I am using the narrowPeak file from macs2 output and plotting the data using chepSeeker from R, but the output figure is not that nice. I figured out that bigwig files look better when plotted.

Does anyone know how to generate bigwig files from Macs2 output? I tried using the function macs2 bdgcmp but I'm not sure if it does the same function as peakcall.

And I would accept any recommendations about plotting chip-seq peaks as well.

Answer 1

[Ian]

Hi,

This is the method I use:

# get genome chromosome sizes (assuming it is a UCSC genome, otherwise this is a tab delimited file with chromosome name in the first column and length in the second):
fetchChromSizes hg38 > hg38.chrom.sizes

# bedClip makes sure regions don't go off the end of the chromosome
bedClip macs2.bdg genome.chrom.sizes macs2_clipped.bdg

# make a bigWig
bedGraphToBigWig macs2_clipped.bdg genome.chrom.sizes macs2.bigWig

You can download these programs from UCSC: http://hgdownload.soe.ucsc.edu/admin/exe/

Useful to use MACS2 --SPMR if you are comparing between tracks.

Hope this helps.

[Alex S]

Hi,

Which bdg from MACS2 do you use? Do you run it using macs2 callpeak, or another function? I don't think I got any bdg from callpeak.

Thanks